A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration


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Documentation for package ‘PepMapViz’ version 1.1.0

Help Pages

calculate_all_Area Calculate Area/Intensity for the whole input sequence dataframe
calculate_all_PSM Calculate Spectra Count (PSM) for the whole input sequence dataframe
calculate_Area Calculate Area/Intensity for one row of the input sequence dataframe
calculate_PSM Calculate Spectra Count (PSM) for one row of the input sequence dataframe
combine_files_from_folder Combine CSV and TXT Files from a Folder
convert_to_regex_pattern Convert Peptide Sequence to Regex Pattern
create_peptide_plot Create a peptide Plot
match_and_calculate_positions Match peptide sequence with provided sequence and calculate positions
obtain_mod Obtain post translational modification(PTM) information from Peptide data based on the specified data type
obtain_mod_Comet Obtain modification information from Peptide data generated by Comet
obtain_mod_DIANN Obtain modification information from Peptide data generated by DIA-NN
obtain_mod_Maxquant Obtain modification information from Peptide data generated by Maxquant
obtain_mod_MSFragger Obtain modification information from Peptide data generated by MSFragger
obtain_mod_mzIdenML Obtain modification information from Peptide data generated by mzIdenML
obtain_mod_mzTab Obtain modification information from Peptide data generated by mzTab
obtain_mod_PEAKS Obtain modification information from Peptide data generated by PEAKS
obtain_mod_Skyline Obtain modification information from Peptide data generated by Skyline
obtain_mod_Spectronaut Obtain modification information from Peptide data generated by Spectronaut
peptide_quantification Peptide Quantification
run_pepmap_app Launch PepMapViz Shiny Application
strip_sequence Strip peptide sequences based on the specified data type
strip_sequence_Comet Strip sequence from Comet outputs
strip_sequence_DIANN Strip sequence from DIANN outputs
strip_sequence_Maxquant Strip sequence from Maxquant outputs
strip_sequence_MSFragger Strip sequence from MSFragger outputs
strip_sequence_PEAKS Strip sequence from PEAKS outputs
strip_sequence_Skyline Strip sequence from Skyline outputs
strip_sequence_Spectronaut Strip sequence from Spectronaut outputs